Is there a way to have uMatrix enable all instances of youtube.com no matter which website uses it?
Sure.
The trick is to create rules in the global scope, so that these rules apply everywhere.
You can select the current scope for which rules will be applied with the top-left cell: click on it, a drop list will appear from which the scope can be selected.
For example, I went to your first example site, selected the global scope (identified with “*”), then created the rules to make the embedded Youtube video work:
What is left to do is save the rules (using the padlock), and a good habit is to select back the local scope to be sure you do not end up mistakenly creating rules in the global scope.
The rules can also be added manually (this is the rules created using the UI above) in the My rules pane in the dashboard:
* youtube.com * allow
* youtube.com frame allow
* ytimg.com * allow
* googlevideo.com * allow
Then click Commit to make them permanent. The first item in a rule is the origin, i.e. where the rule should apply. * = everywhere, aka global scope.
(Edit: added missing rule for googlevideo.com: you will need to select it in the UI or add it manually – embedded Youtube videos won’t work without it.)